A. Chatha, S. Naz, S. Iqbal, Azka Kiran, Maria Lateef, Unab Zahra, Fatima Yasmin, Nimra Amjad, Ammara Javaid
Heavy metals have an enduring presence, risky characteristics, and the propensity to accumulate in the environment. This is why heavy metal toxics are widely acknowledged as harmful environmental pollutants. Heavy metals damage both aquatic and terrestrial ecosystems, posing a major risk to the environment and human health. Four freshwater fish species namely Labeo rohita, Catla catla, Hypophthalmichthys molitrix, and Ctenopharyngodon idella were the focus of this investigation. This study investigated the potential genotoxic effects of lead (Pb), copper (Cu), and cadmium (Cd) on the above fish species through the application of comet assay test. The fish were exposed to these metals at four distinct concentrations (19%, 24%, 31%, and 50% of the LC50) over the course of 40 days. All four fish species were exposed to metals to varying degrees, according to the genetic damage index, cumulative tail length of comets, and the proportion of damaged cells. In contrast to Catla catla, Hypophthalmichthys molitrix had the highest prevalence of DNA damage. The current study suggests that the presence of these particular metals in Pakistan's aquatic ecosystems may have an adverse effect on the DNA of the country's fish species. Metals cause damage to DNA in fibroblast cells through distinct mechanisms when present in water, air, and soil. Comet assay test has a remarkable sensitivity that helps to identify extremely low amounts of DNA damage. Out of the four fish species, Ctenopharyngodon idella showed higher levels of damaged cells, a higher genetic damage index, and a cumulative comet tail length as compared to others. All four fish species experienced a significant increase in DNA damage, genetic damage index, and comet tail length at 50% concentration of metals LC50.
重金属具有持久性、危险性和在环境中累积的倾向。因此，重金属毒物被公认为有害的环境污染物。重金属会破坏水生和陆地生态系统，对环境和人类健康构成重大威胁。本研究以 Labeo rohita、Catla catla、Hypophthalmichthys molitrix 和 Ctenopharyngodon idella 四种淡水鱼为研究对象。本研究通过彗星试验研究了铅（Pb）、铜（Cu）和镉（Cd）对上述鱼类物种的潜在基因毒性影响。鱼类暴露于四种不同浓度的金属（分别为半数致死浓度的 19%、24%、31% 和 50%）40 天。根据遗传损伤指数、彗星累积尾长和受损细胞比例，所有四种鱼类都受到了不同程度的金属暴露。与 Catla catla 相反，Hypophthalmichthys molitrix 的 DNA 损伤率最高。目前的研究表明，巴基斯坦水生生态系统中存在的这些特定金属可能会对该国鱼类物种的 DNA 产生不利影响。当金属存在于水、空气和土壤中时，会通过不同的机制对成纤维细胞的 DNA 造成损伤。彗星检测法具有极高的灵敏度，有助于识别极低量的 DNA 损伤。在四种鱼类中，栉水母（Ctenopharyngodon idella）与其他鱼类相比，受损细胞水平更高，遗传损伤指数更高，彗星尾的累积长度也更长。在半数致死浓度为 50%的金属浓度下，所有四种鱼类的 DNA 损伤、遗传损伤指数和彗星尾长度都有明显增加。
{"title":"Detection of DNA Damage in Fish using Comet Assay","authors":"A. Chatha, S. Naz, S. Iqbal, Azka Kiran, Maria Lateef, Unab Zahra, Fatima Yasmin, Nimra Amjad, Ammara Javaid","doi":"10.32350/cto.41.01","DOIUrl":"https://doi.org/10.32350/cto.41.01","url":null,"abstract":"Heavy metals have an enduring presence, risky characteristics, and the propensity to accumulate in the environment. This is why heavy metal toxics are widely acknowledged as harmful environmental pollutants. Heavy metals damage both aquatic and terrestrial ecosystems, posing a major risk to the environment and human health. Four freshwater fish species namely Labeo rohita, Catla catla, Hypophthalmichthys molitrix, and Ctenopharyngodon idella were the focus of this investigation. This study investigated the potential genotoxic effects of lead (Pb), copper (Cu), and cadmium (Cd) on the above fish species through the application of comet assay test. The fish were exposed to these metals at four distinct concentrations (19%, 24%, 31%, and 50% of the LC50) over the course of 40 days. All four fish species were exposed to metals to varying degrees, according to the genetic damage index, cumulative tail length of comets, and the proportion of damaged cells. In contrast to Catla catla, Hypophthalmichthys molitrix had the highest prevalence of DNA damage. The current study suggests that the presence of these particular metals in Pakistan's aquatic ecosystems may have an adverse effect on the DNA of the country's fish species. Metals cause damage to DNA in fibroblast cells through distinct mechanisms when present in water, air, and soil. Comet assay test has a remarkable sensitivity that helps to identify extremely low amounts of DNA damage. Out of the four fish species, Ctenopharyngodon idella showed higher levels of damaged cells, a higher genetic damage index, and a cumulative comet tail length as compared to others. All four fish species experienced a significant increase in DNA damage, genetic damage index, and comet tail length at 50% concentration of metals LC50.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139290437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qurat Ul Ain Haider, Hafsa Saeed, Wajiha Ikram, Usama Ikram, Misbah Hussain
Hypertension is a multifactorial disease characterized by high blood pressure in blood vessels. It is caused by the dysregulation of renin angiotensin aldosterone system (RAAS). It is a major risk factor for other metabolic diseases including cardiovascular diseases, diabetes, and others. Various RAAS targeting drugs such as losartan are prescribed as the first line therapy to treat hypertension. However, their efficacy varies among individuals owing to genetic variations in drug binding substrates or drug metabolizing enzymes, which convert the prodrug to active drug. CYP2C9 gene encodes for an enzyme which metabolizes losartan. Various studies have concluded that genetic variations in CYP2C9 affect the response of losartan due to the variation in its metabolism. Thus, the current study aimed to check the effect of CYP2C9 rs2860905 G>A polymorphism on the efficacy of losartan. For this purpose, a total of 48 subjects were selected and genotyped for rs2860905 polymorphism using in-house developed tetra-ARMS-PCR. The subjects were divided into responding (n=34) and non-responding (n=14) groups on the basis of their blood pressure after treatment with losartan. Statistical analysis demonstrated that rs2860905 GG genotype was more prevalent in the responding group as compared to the non-responding group (50% vs. 36%). Multinomial regression analysis showed that the carriers of GA or AA genotype did not respond to losartan treatment efficiently as compared to those of GG genotype. However, these results could not achieve statistical significance. To conclude, CYP2C9 rs2860905 G>A polymorphism does not affect the efficacy of losartan in Pakistani hypertensive subjects.
{"title":"Effect of CYP2C9 rs2860905 Polymorphism on the Efficacy of Losartan in Pakistani Hypertensive Patients","authors":"Qurat Ul Ain Haider, Hafsa Saeed, Wajiha Ikram, Usama Ikram, Misbah Hussain","doi":"10.32350/cto.32.05","DOIUrl":"https://doi.org/10.32350/cto.32.05","url":null,"abstract":"Hypertension is a multifactorial disease characterized by high blood pressure in blood vessels. It is caused by the dysregulation of renin angiotensin aldosterone system (RAAS). It is a major risk factor for other metabolic diseases including cardiovascular diseases, diabetes, and others. Various RAAS targeting drugs such as losartan are prescribed as the first line therapy to treat hypertension. However, their efficacy varies among individuals owing to genetic variations in drug binding substrates or drug metabolizing enzymes, which convert the prodrug to active drug. CYP2C9 gene encodes for an enzyme which metabolizes losartan. Various studies have concluded that genetic variations in CYP2C9 affect the response of losartan due to the variation in its metabolism. Thus, the current study aimed to check the effect of CYP2C9 rs2860905 G>A polymorphism on the efficacy of losartan. For this purpose, a total of 48 subjects were selected and genotyped for rs2860905 polymorphism using in-house developed tetra-ARMS-PCR. The subjects were divided into responding (n=34) and non-responding (n=14) groups on the basis of their blood pressure after treatment with losartan. Statistical analysis demonstrated that rs2860905 GG genotype was more prevalent in the responding group as compared to the non-responding group (50% vs. 36%). Multinomial regression analysis showed that the carriers of GA or AA genotype did not respond to losartan treatment efficiently as compared to those of GG genotype. However, these results could not achieve statistical significance. To conclude, CYP2C9 rs2860905 G>A polymorphism does not affect the efficacy of losartan in Pakistani hypertensive subjects.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134981665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Antioxidant activity of 12 species, of which one was Cuscuta reflexa Roxb. which belongs to the family of Cuscutaceae as well as 11 of Convolvulaceae, collected from district Bhimber, Mirpur and Kotli were measured by using ABTS, DPPH and FRAP assay. The total phenol and flavonoid contents of the whole plant of all the selected species were investigated. Ipomoea eriocarpa showed a comparatively higher amount of total polyphenols (0.98 ± 0.073 mg/gdw). The maximum DPPH value was shown by Ipomoea carnea Jacq (5.6%) and the minimum value was shown by Convolvulus arvensis L. extracts (3.0 %). ABTS was the highest by Convolvulus prostrastus and the lowest by Ipomoea carnea. In FRAP assay, the highest value was 2.75 by Ipomoea hederacia and the lowest value was 0.31 by I. arachnosperma Welw. The antifungal and antibacterial activity of the methanolic extracts of the whole plant of all the selected species was carried out by using both bacterial and fungal strains. Two gram positive bacteria namely Staphylococcus aureus and Bacillus subtilis, two gram negative bacteria namely E. coli and Pseudomonas aeruginosa, two fungal strains of Aspergillus niger and Aspergillus oryzae were used to carry out antimicrobial activity. For the comparison of inhibition zones showed by plant extracts against bacterial and fungal strains. Erythromycin, tetracycline and cefoparazone were used as standard for bacterial strains. Moreover, fungivine and Terbinafine were used as standard antibiotics against fungal strains. Among fungal strains, the highest zone of inhibition was shown by Cuscuta reflexa Roxb. extract against Aspergillus niger, that is 5.55±0.3, while the lowest zone of inhibition, that is, 0.60±0.28mm was shown by Evolvulus alsinoides (L.) extract against Aspergillus oryzae. Plants from the Convolvulaceae family have had frequent traditional uses for different therapeutic purposes. Furthermore, all plants selected for this study showed strong antimicrobial, antifungal, and antioxidant activity. Their further detailed phytochemical studies can help to develop plant-based therapeutic agents
{"title":"Antioxidant and Antimicrobial Activity of Cuscuta reflexa ROXB. and Few Members of Family Convolvulaceae","authors":"Qumqum Noshad, Muhammad Ajaib, Aysha Kiran","doi":"10.32350/cto.32.01","DOIUrl":"https://doi.org/10.32350/cto.32.01","url":null,"abstract":"Antioxidant activity of 12 species, of which one was Cuscuta reflexa Roxb. which belongs to the family of Cuscutaceae as well as 11 of Convolvulaceae, collected from district Bhimber, Mirpur and Kotli were measured by using ABTS, DPPH and FRAP assay. The total phenol and flavonoid contents of the whole plant of all the selected species were investigated. Ipomoea eriocarpa showed a comparatively higher amount of total polyphenols (0.98 ± 0.073 mg/gdw). The maximum DPPH value was shown by Ipomoea carnea Jacq (5.6%) and the minimum value was shown by Convolvulus arvensis L. extracts (3.0 %). ABTS was the highest by Convolvulus prostrastus and the lowest by Ipomoea carnea. In FRAP assay, the highest value was 2.75 by Ipomoea hederacia and the lowest value was 0.31 by I. arachnosperma Welw. The antifungal and antibacterial activity of the methanolic extracts of the whole plant of all the selected species was carried out by using both bacterial and fungal strains. Two gram positive bacteria namely Staphylococcus aureus and Bacillus subtilis, two gram negative bacteria namely E. coli and Pseudomonas aeruginosa, two fungal strains of Aspergillus niger and Aspergillus oryzae were used to carry out antimicrobial activity. For the comparison of inhibition zones showed by plant extracts against bacterial and fungal strains. Erythromycin, tetracycline and cefoparazone were used as standard for bacterial strains. Moreover, fungivine and Terbinafine were used as standard antibiotics against fungal strains. Among fungal strains, the highest zone of inhibition was shown by Cuscuta reflexa Roxb. extract against Aspergillus niger, that is 5.55±0.3, while the lowest zone of inhibition, that is, 0.60±0.28mm was shown by Evolvulus alsinoides (L.) extract against Aspergillus oryzae. Plants from the Convolvulaceae family have had frequent traditional uses for different therapeutic purposes. Furthermore, all plants selected for this study showed strong antimicrobial, antifungal, and antioxidant activity. Their further detailed phytochemical studies can help to develop plant-based therapeutic agents","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"158 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134982974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alzheimer’s disease (AD) is an irreversible and progressive neurodegenerative disorder. The brain mechanisms involved in this disease remain largely unknown. Hence, this study used the integrated bioinformatics approach to analyze a high throughput sequencing dataset (GSE162873) in order to identify the potential biomarkers involved in the pathophysiology of this disease. DESeq2 package was used for the identification of differentially expressed genes (DEGs) from both healthy and diseased patients. DAVID, a web-based bioinformatics resource, was used to perform functional enrichment analysis. StringApp plugin in Cytoscape was utilized to construct the protein-protein interaction (PPI) networks, whereas hub genes were identified through cytoHubba. MCODE was used to perform module analysis, ClueGO to evaluate the KEGG pathways enriched in modules, and miRNet platform for the interaction analysis of miRNAs and hub genes. Drug-genes interaction analysis was performed using DGIdb resource to find out the related drugs. A total of 652 DEGs were screened which were significantly enriched in GO terms. KEGG pathways analysis showed that PI3K-Akt signaling, hippo signaling, MAPK signaling, TGF-beta signaling, and sphingolipid signaling were significantly enriched pathways. A total of 12 hub genes were found to be significantly interacting with miR-603, miR-10b-5p, miR-124-3p, and miR-1-3p, and some FDA approved drugs. The current study provided an insight into the molecular mechanisms of AD and identified some potential biomarker genes, their pathways, miRNAs, and drugs which might be useful for diagnostic and therapeutic purposes.
{"title":"Identification and Analysis of Hub Genes and Biological Pathways Involved in Alzheimer’s Disease (AD) Using Transcriptomics Dataset","authors":"Humaira Amin, Asghar Shabbir, Khuram Shahzad","doi":"10.32350/cto.32.04","DOIUrl":"https://doi.org/10.32350/cto.32.04","url":null,"abstract":"Alzheimer’s disease (AD) is an irreversible and progressive neurodegenerative disorder. The brain mechanisms involved in this disease remain largely unknown. Hence, this study used the integrated bioinformatics approach to analyze a high throughput sequencing dataset (GSE162873) in order to identify the potential biomarkers involved in the pathophysiology of this disease. DESeq2 package was used for the identification of differentially expressed genes (DEGs) from both healthy and diseased patients. DAVID, a web-based bioinformatics resource, was used to perform functional enrichment analysis. StringApp plugin in Cytoscape was utilized to construct the protein-protein interaction (PPI) networks, whereas hub genes were identified through cytoHubba. MCODE was used to perform module analysis, ClueGO to evaluate the KEGG pathways enriched in modules, and miRNet platform for the interaction analysis of miRNAs and hub genes. Drug-genes interaction analysis was performed using DGIdb resource to find out the related drugs. A total of 652 DEGs were screened which were significantly enriched in GO terms. KEGG pathways analysis showed that PI3K-Akt signaling, hippo signaling, MAPK signaling, TGF-beta signaling, and sphingolipid signaling were significantly enriched pathways. A total of 12 hub genes were found to be significantly interacting with miR-603, miR-10b-5p, miR-124-3p, and miR-1-3p, and some FDA approved drugs. The current study provided an insight into the molecular mechanisms of AD and identified some potential biomarker genes, their pathways, miRNAs, and drugs which might be useful for diagnostic and therapeutic purposes.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134982976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jian Yang, Xiao Wang, Jie Xue, Yundong Gao, Jianbin Li
The current study conducted a preliminary investigation of genetic correlations in Chinese Holstein bulls to improve their semen quantity and quality by indirect selection of conformation traits. The results of seven semen traits and nine conformation traits showed that the heritability estimates of semen traits ranged from 0.24 (post-thaw motility) to 0.63 (volume per ejaculation), while the conformation traits ranged from 0.29 (pin width) to 0.80 (withers height). Phenotypic correlation between scrotal circumference (SC) and semen concentration per ejaculation (SCPE), SC and total number of sperm per ejaculation (TNS), and SC and total number of motile sperm per ejaculation (TNMS) was 0.22, 0.25, and 0.24, respectively. Genetic correlation between SC and SCPE, SC and TNS, and SC and TNMS was 0.41, 0.40, and 0.38, respectively. To summarize, moderate or high heritability of semen traits indicated that genetic improvement of semen quality by selection is feasible, where SC could be a useful trait for indirect selection or as correlated information to improve semen quantity and production.
{"title":"Genetic Correlation of Conformation Traits with Semen Traits in Chinese Holstein Bulls: A Preliminary Investigation","authors":"Jian Yang, Xiao Wang, Jie Xue, Yundong Gao, Jianbin Li","doi":"10.32350/cto.32.03","DOIUrl":"https://doi.org/10.32350/cto.32.03","url":null,"abstract":"The current study conducted a preliminary investigation of genetic correlations in Chinese Holstein bulls to improve their semen quantity and quality by indirect selection of conformation traits. The results of seven semen traits and nine conformation traits showed that the heritability estimates of semen traits ranged from 0.24 (post-thaw motility) to 0.63 (volume per ejaculation), while the conformation traits ranged from 0.29 (pin width) to 0.80 (withers height). Phenotypic correlation between scrotal circumference (SC) and semen concentration per ejaculation (SCPE), SC and total number of sperm per ejaculation (TNS), and SC and total number of motile sperm per ejaculation (TNMS) was 0.22, 0.25, and 0.24, respectively. Genetic correlation between SC and SCPE, SC and TNS, and SC and TNMS was 0.41, 0.40, and 0.38, respectively. To summarize, moderate or high heritability of semen traits indicated that genetic improvement of semen quality by selection is feasible, where SC could be a useful trait for indirect selection or as correlated information to improve semen quantity and production.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134982975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The invention of next generation technologies which are aimed to resolve human health issues is gaining importance. Micro-RNAs (miRNAs) analysis is are an important discovery in the field of molecular biology. miRNAs are small endogenous RNAs which are involved in the regulation of post-transcriptional genes expression. They have been identified in different organisms, such as viruses, plants, human beings, and animals by using computational analysis tools. miRNAs are best predicted by next generation sequencing. They play a role as potential biomarkers in developmental processes. They are important therapeutic agents which play their role in diseases, such as cardiovascular, autoimmune, cancer, and neural degenerative diseases. The current study aimed to explore miRNAs and their clinical applications. For this purpose, miRNAs were analyzed as therapeutic agents and molecular biomarkers.
{"title":"MicroRNAs: An Overview of their Discovery, Biogenesis, Computational Prediction, and Potential Clinical Applications","authors":"Iqra Kainat, Sara Khan, Anam Zahra, Misbah Saleem","doi":"10.32350/cto.32.02","DOIUrl":"https://doi.org/10.32350/cto.32.02","url":null,"abstract":"The invention of next generation technologies which are aimed to resolve human health issues is gaining importance. Micro-RNAs (miRNAs) analysis is are an important discovery in the field of molecular biology. miRNAs are small endogenous RNAs which are involved in the regulation of post-transcriptional genes expression. They have been identified in different organisms, such as viruses, plants, human beings, and animals by using computational analysis tools. miRNAs are best predicted by next generation sequencing. They play a role as potential biomarkers in developmental processes. They are important therapeutic agents which play their role in diseases, such as cardiovascular, autoimmune, cancer, and neural degenerative diseases. The current study aimed to explore miRNAs and their clinical applications. For this purpose, miRNAs were analyzed as therapeutic agents and molecular biomarkers.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"70 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134981664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dr. Saima Naz, A. Chatha, Urooj Nazir, S. Iqbal, D. Danabaş
The current study aims to construct a thorough barcoding reference database of fishes in the Head Taunsa Barrage and assess the usefulness of employing the COI gene for fish species identification. A total of 15 genera, 10 families, and 7 orders of fish were used to collect a total of 19 mitochondrial COI barcode sequences. These sequences had an average length of 800 base pairs. Within species, genera, families, orders, and classes, the average Kimura two-parameter (K2P) distances were 0.97%, 0.99%, 1.23%, and 1.26%, respectively. According to their taxonomic classification, species were commonly clustered in the K2P neighbor-joining trees based on the sequence. DNA barcoding was employed in this study to identify species with a high degree of accuracy. Moreover, it was concluded that COI sequencing can be used to recognize fish species.
{"title":"Morphological and Genetic Identification of Head Taunsa Barrage Fish Species","authors":"Dr. Saima Naz, A. Chatha, Urooj Nazir, S. Iqbal, D. Danabaş","doi":"10.32350/cto.31.03","DOIUrl":"https://doi.org/10.32350/cto.31.03","url":null,"abstract":"The current study aims to construct a thorough barcoding reference database of fishes in the Head Taunsa Barrage and assess the usefulness of employing the COI gene for fish species identification. A total of 15 genera, 10 families, and 7 orders of fish were used to collect a total of 19 mitochondrial COI barcode sequences. These sequences had an average length of 800 base pairs. Within species, genera, families, orders, and classes, the average Kimura two-parameter (K2P) distances were 0.97%, 0.99%, 1.23%, and 1.26%, respectively. According to their taxonomic classification, species were commonly clustered in the K2P neighbor-joining trees based on the sequence. DNA barcoding was employed in this study to identify species with a high degree of accuracy. Moreover, it was concluded that COI sequencing can be used to recognize fish species.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125089016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
H. Sadia, Waqas Ahmed Khan, Misbah Hussain, Iqra Murtza
Hypertrophic cardiomyopathy (HCM) is a common and complex, genetically inherited, cardiovascular disorder. It is typically inherited in an autosomal dominant manner with variable penetrance and mutable expression. Mutations in MYBPC3 gene is one of the genetic causes of HCM. Only 0.2% of general population suffers from HCM. The MYBPC3 gene provides instructions for making cardiac myosin binding protein C, which is imperative for the maintenance and regulation of normal cardiac functions. This study aims to explore the reported SNP rs1052373 from exon 30 of MYBPC3 gene in the population of Punjab, Pakistan. The reported SNP rs1052373 was analysed using Tetra Amplification Refractory Mutation System Polymerase Chain Reaction (T-ARMS-PCR) to find the allelic frequency in the selected population. T-ARMS-PCR is a cost effective, flexible, rapid, and accurate tool for genotyping. The specific sequences of MYBPC3 gene from exons 30 and 31 and introns 29, 30, and 31 were retrieved from NCBI (https://www.ncbi.nlm.nih.gov/). A tetra primer designing tool known as Primer 1 (http://primer1.soton.ac.uk/primer1.html) was used to design the primers for the targeted region of MYBPC3 gene. In this study, the genotyping of previously reported SNP rs1052373 showed variation in the disease group, giving CC, CT, and TT genotypes with the frequency of 0.04. The genotyping analysis of rs1052373 showed that the allelic frequency of homozygous condition T/T was 0.02 and the allelic frequency of heterozygous condition C/T was 0.02 in disease group as compared to the control group. In the latter, the homozygous T/T and heterozygous C/T genotypes were not observed in any individuals. All the individuals in control group carried homozygous C/C genotype. While, the frequency of homozygous C/C genotype was 0.96 in disease group. The findings of this study would help to find novel molecular markers for HCM diagnosis.
{"title":"Development of T-ARMS-PCR to Detect MYBPC3 Gene Variation in Hypertrophic Cardiomyopathy (HCM) Patients","authors":"H. Sadia, Waqas Ahmed Khan, Misbah Hussain, Iqra Murtza","doi":"10.32350/cto.31.04","DOIUrl":"https://doi.org/10.32350/cto.31.04","url":null,"abstract":"Hypertrophic cardiomyopathy (HCM) is a common and complex, genetically inherited, cardiovascular disorder. It is typically inherited in an autosomal dominant manner with variable penetrance and mutable expression. Mutations in MYBPC3 gene is one of the genetic causes of HCM. Only 0.2% of general population suffers from HCM. The MYBPC3 gene provides instructions for making cardiac myosin binding protein C, which is imperative for the maintenance and regulation of normal cardiac functions. This study aims to explore the reported SNP rs1052373 from exon 30 of MYBPC3 gene in the population of Punjab, Pakistan. The reported SNP rs1052373 was analysed using Tetra Amplification Refractory Mutation System Polymerase Chain Reaction (T-ARMS-PCR) to find the allelic frequency in the selected population. T-ARMS-PCR is a cost effective, flexible, rapid, and accurate tool for genotyping. The specific sequences of MYBPC3 gene from exons 30 and 31 and introns 29, 30, and 31 were retrieved from NCBI (https://www.ncbi.nlm.nih.gov/). A tetra primer designing tool known as Primer 1 (http://primer1.soton.ac.uk/primer1.html) was used to design the primers for the targeted region of MYBPC3 gene. In this study, the genotyping of previously reported SNP rs1052373 showed variation in the disease group, giving CC, CT, and TT genotypes with the frequency of 0.04. The genotyping analysis of rs1052373 showed that the allelic frequency of homozygous condition T/T was 0.02 and the allelic frequency of heterozygous condition C/T was 0.02 in disease group as compared to the control group. In the latter, the homozygous T/T and heterozygous C/T genotypes were not observed in any individuals. All the individuals in control group carried homozygous C/C genotype. While, the frequency of homozygous C/C genotype was 0.96 in disease group. The findings of this study would help to find novel molecular markers for HCM diagnosis.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"8 11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129825979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Artificial intelligence (AI) has made significant strides in recent years toward resolving a wide range of biological issues, including a number of occurrences connected to cancer. Deep learning is an adaptable sector of AI that enables the automatic extraction of features. It is increasingly being used in various fields of cancer research, both scientific and clinical. In this study, several current applications of AI in oncology, including the situations in which deep learning has effectively addressed intractable disputes, are discussed. This study also discusses the challenges that need to be surmounted before such an application of AI may be implemented more broadly. Similarly, it brings to light resources and data sets that can assist in maximizing the potential of AI. Essential insights in oncology may be generated based on the development of novel methodologies and uses of AI, making it possible for substantial changes to be made to clinical practice.
{"title":"Current State of Artificial Intelligence (AI) in Oncology: A Review","authors":"Aqib Ali, Samreen Naeem, Sania Anam, M. Ahmed","doi":"10.32350/cto.31.01","DOIUrl":"https://doi.org/10.32350/cto.31.01","url":null,"abstract":"Artificial intelligence (AI) has made significant strides in recent years toward resolving a wide range of biological issues, including a number of occurrences connected to cancer. Deep learning is an adaptable sector of AI that enables the automatic extraction of features. It is increasingly being used in various fields of cancer research, both scientific and clinical. In this study, several current applications of AI in oncology, including the situations in which deep learning has effectively addressed intractable disputes, are discussed. This study also discusses the challenges that need to be surmounted before such an application of AI may be implemented more broadly. Similarly, it brings to light resources and data sets that can assist in maximizing the potential of AI. Essential insights in oncology may be generated based on the development of novel methodologies and uses of AI, making it possible for substantial changes to be made to clinical practice.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125724566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zainab Asif Mirza, A. Naeem, Aamna Syed, R. Mateen, M. I. Fareed, Dr. Mureed Husaain
Desbuquois dysplasia (DBQD) is an autosomal recessive chondrodysplasia that belongs to the multiple dislocation group and causes parental and afterbirth growth retardation, hand and proximal femur abnormalities, joint laxity, and scoliosis. Several missense and splice site mutations in CANT1 gene are linked with the development of DBQD. In silico approaches can predict the pathogenic variations causing hereditary diseases. Hence, in the current study, in silico analysis was used to forecast the variants of CANT1 gene that harm the functionality of calcium-dependent nucleotidase. A total of 281 variants with uncertain significance, retrieved from the gnomAD, dbSNP, ClinVar, and Variation Viewer databases, were analyzed using CADD, Meta SNP, CAPiCE, and Condel to predict 61 highly pathogenic variants. Stability change predicting computational tools were applied to filter 19 highly pathogenic amino acid variants that impact protein dynamics via sample conformation or during vibrational entropy. UCSF Chimera was used for interactive visualization and analysis of unwanted interaction among 5 variants in the molecular structure of the protein. Ligand binding computational tools were used to interpret the protein-ligand interactions. A total of three (3) post-translational modification sites were also predictably disrupted by 16 variants. Spice and HSF 3.1 tools were applied to 95 variants to check their disease-causing potential. The variants of the gene were analyzed using computational tools based on different algorithms. The most damaging variants of CANT1 gene that can affect the functionality and stability of the protein were predicted. It was determined that an extensive in silico analysis can determine the likely pathogenic variations for further in vitro experimental analysis.
{"title":"In Silico Analysis to Predict the Pathogenic Variants of CANT1 Gene Causing Desbuquios Dysplasia (DBQD) Type 1","authors":"Zainab Asif Mirza, A. Naeem, Aamna Syed, R. Mateen, M. I. Fareed, Dr. Mureed Husaain","doi":"10.32350/cto.31.02","DOIUrl":"https://doi.org/10.32350/cto.31.02","url":null,"abstract":"Desbuquois dysplasia (DBQD) is an autosomal recessive chondrodysplasia that belongs to the multiple dislocation group and causes parental and afterbirth growth retardation, hand and proximal femur abnormalities, joint laxity, and scoliosis. Several missense and splice site mutations in CANT1 gene are linked with the development of DBQD. In silico approaches can predict the pathogenic variations causing hereditary diseases. Hence, in the current study, in silico analysis was used to forecast the variants of CANT1 gene that harm the functionality of calcium-dependent nucleotidase. A total of 281 variants with uncertain significance, retrieved from the gnomAD, dbSNP, ClinVar, and Variation Viewer databases, were analyzed using CADD, Meta SNP, CAPiCE, and Condel to predict 61 highly pathogenic variants. Stability change predicting computational tools were applied to filter 19 highly pathogenic amino acid variants that impact protein dynamics via sample conformation or during vibrational entropy. UCSF Chimera was used for interactive visualization and analysis of unwanted interaction among 5 variants in the molecular structure of the protein. Ligand binding computational tools were used to interpret the protein-ligand interactions. A total of three (3) post-translational modification sites were also predictably disrupted by 16 variants. Spice and HSF 3.1 tools were applied to 95 variants to check their disease-causing potential. The variants of the gene were analyzed using computational tools based on different algorithms. The most damaging variants of CANT1 gene that can affect the functionality and stability of the protein were predicted. It was determined that an extensive in silico analysis can determine the likely pathogenic variations for further in vitro experimental analysis.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133265065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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